Protesters in the US hold signs opposing Monsanto and the use of glyphosate.
Photograph: Alex Milan Tracy/Demotix/Corbis

The European Food and Safety Authority (Efsa) has removed barriers to the relicensing of glyphosate, a best-selling herbicide, despite World Health Organisation (WHO) warnings that the substance is “probably carcinogenic to humans”.

The ruling opens the door to a new 10-year licence for glyphosate across Europe, although the authority set a threshold for exposure to the substance of of 0.5mg per kg of body weight for the first time.

“Glyphosate is unlikely to pose a carcinogenic hazard to humans and the evidence does not support classification with regard to its carcinogenic potential,” the Efsa assessment found.

But a row immediately broke out over its scientific basis, which relied on six industry-funded studies that have not been published in full.

The studies were submitted on behalf of an industry alliance called the Glyphosate Task Force by the GM multinational Monsanto, which also dealt with media inquiries about the group until recently.

Richard Garnett, the task force’s chair, described the Efsa ruling as “a key milestone” in the assessment process.

“It confirms the previous evaluations of glyphosate by regulatory authorities around the world, which have consistently concluded that the application of glyphosate poses no unacceptable risk to human health, animals or the environment,” he said.

Garnett has worked as Monsanto’s lead officer for crop protection regulatory affairs since 2003.

David Carpintero, a Monsanto spokesman, said the firm had a “special role” in the group as the first point of contact with regulatory authorities.

“We have a strong interest,” he told the Guardian. “We are a leading company in this product.”

But funding for the group was shared equally with other alliance members, including Syngenta, Dow and Barclays Chemicals, he added.

Glyphosate is a key ingredient in Monsanto’s multi-billion dollar RoundUp weedkiller brand and its relicensing has acted as a lightning rod for anger over GM foods, pesticide use and the influence of industry on EU policymaking.

Shortly before the announcement, an Avaaz petition signed by 1.4 million people was handed in to the European commission, calling on the bloc not to relicense.

Alice Jay, Avaaz’s campaign director, said Monsanto’s RoundUp, which is meant to be used on herbicide-tolerant GM crops, could be “the new DDT”.

But Jose Tarazona, the head of Efsa’s pesticides unit, insisted that its 6,000-page assessment had been exhaustive, comprehensive and opposed by only one Swedish member of the peer review expert group of scientists and national experts.

“We included all the studies that have been assessed by the International Agency for Research on Cancer (IARC)”, he said, referring to the WHO’s assessment. “We also detected other studies – some very key – and so we had more evidence and information and a we had a different set of criteria.”

Efsa said the WHO scientists came to a different conclusion because they studied generic “glyphosate-based” compounds rather than the active substance, glyphosate, in isolation.

But consumers are unlikely to come into the product in its “pure” form, and environmentalists say the studies cited by IARC, concerning glyphosate’s cancer-causing effects on mice, involved glyphosate alone.

An analysis by the Pesticide Action Network also criticised some industry studies for not comparing control groups of mice that had been exposed to glyphosate – and had high incidences of tumours – with similar groups that had not.

By using historic surveys of different rodents in different labs for comparison, a conclusion could be drawn that the tumour incidences were not significant, the group said.

The Efsa assessment was welcomed by farmers’ groups, who pointed to ecological benefits.

“Glyphosate is an important part of a farmer’s and gardener’s toolbox,” said Nick von Westenholz, CEO of the Crop Protection Association.

“It is particularly important in minimising food waste by controlling a broad spectrum of weeds and therefore reducing the need for ploughing of soils.